Nicholas Wade Writes about Genomes and Evolution

His fellow science writers often think that Nicholas Wade is among the best of their ilk. Wade writes for the New York Times and his latest article is: A Decade Later, Genetic Map Yields Few New Cures. A couple of paragraphs from that article deserve some kind of award.

But while 10 years of the genome may have produced little for medicine, the story for basic science has been quite different. Research on the genome has transformed biology, producing a steady string of surprises. First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly. The barely visible roundworm needs 20,000 genes that make proteins, the working parts of cells, whereas humans, apparently so much higher on the evolutionary scale, seem to have only 21,000 protein-coding genes.

The slowly emerging explanation is that humans and other animals have much the same set of protein-coding genes, but the human set is regulated in a much more complicated way, through elaborate use of DNA’s companion molecule, RNA.

Thanks to Jonathan Eisen at The Tree of Life, Nicholas Wade can now add the "Twisted Tree of Life Award" to his many others [Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc].

You see, Wade makes one of the most fundamental errors of evolutionary thinking when he writes about "higher" and "lower" on the "evolutionary scale."

There are two other flaws in his quoted excerpt. First, it did not come as a big surprise to all scientists that humans had about the same number of genes as other animals. That's a myth based on overemphasizing the opinions of some people and underemphasizing the opinions of the experts [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. This is part of what I call The Deflated Ego Problem and it's not endemic. It can be cured by reason.

Second, the explanations for similar numbers of genes in animals come from genetics and developmental biology over the past fifty years. It may have been "slowly emerging" back when I first started teaching but it's now fully emerged and has been for twenty years. Long before the human genome was sequenced we knew that major morphological changes could be caused by small mutations in regulatory sequences. During the 1980s and 1990s it became apparent that animals such as Drosohila and humans shared many important development genes¹ and even more of the genes involved in basic metabolism. This was not a surprise.

It may be true that RNA places a much more important role in regulating gene expression than we thought. The jury is still out on that one. However, even if RNA is part of the regulation picture that fact does not change the basic principle that molecular biologist developed over the past thirty years; namely, that the same basic gene set is just regulated differently in different animals. This is the contribution of Evo-Devo.

There's one other logical flaw made by those with deflated egos. What they're looking for is some specific mechanism that explains the marvelous complexity of humans relative to the "lowly" fruit fly or nematode. What they need in order to satisfy this longing is a mechanism that we have and they don't. As far as I know, there isn't (hardly) anyone who claims that regulatory RNAs have only evolved in humans. The genome sequences of all animals is pointing in the same direction. If there are abundant regulatory RNAs then there are lots in nematodes and fruit flies as well. It's not going to solve the pseudoproblem that Nicholas Wade imagines.

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1. Perhaps you've heard of homeotic genes and HOX genes?

Nature Opens Mouth—Inserts Foot

 
Nature Publishing Group has responded to the potential boycott of its products by the Universities of California [Nature vs. The University of California]. Here's what they have to say for themselves ... [Public statement from Nature Publishing Group regarding subscription renewals at California Digital Library (CDL)].

The implication that NPG is increasing its list prices by massive amounts is entirely untrue. We have been publishing our academic site licence pricing for several years on our librarian gateway. Dollar list price increases have been reasonable (averaging roughly 7 % over 4 years), and publicly available throughout. A 7% cap on annual list price increases is currently in place.

The complication with CDL is that they have been on a very large, unsustainable discount for many years, to the point where other subscribers, both in the US and around the world, are subsidising them. The origins of this discount can be found in the lack of clear definitions around consortia and 'single institute, multisite' subscribers, as well as previous accommodations of CDL's budget limitations.

If we regard CDL as a consortium of multiple libraries (not least suggested by CDL's membership of International Coalition of Library Consortia (ICOLC), and the libraries' ARL listings), the CDL discount on list price is 88%. By their own figures, CDL receives average discounts of 55% from publishers. After several attempts, we are now trying to bring them close to a 50% discount (although this leaves CDL on better terms than many other consortia). We do recognise the situation can be viewed from different perspectives, and we remained committed to ongoing discussions.

Translation: It's completely untrue that NPG is increasing its prices. It's only massively increasing prices for the Universities of California. Price increases for other schools are "only" 7%.

Question: Is it true that the prices to other universities have increased because CDL has been getting a bargain? That's the only way to interpret the statement that, "... other subscribers, both in the US and around the world, are subsidising them"? If so, then if the new contract with CDL results in a huge price increase, doesn't it follow that the prices for all other subscribers should go down? That means the University of Toronto will get a price reduction when CDL and NPG reach agreement, right? Or am I missing something?

Our own projections show CDL will be paying roughly $0.56 per download under the new prices. This represents incredible value for money across any publisher's range of titles. We now call on CDL to reveal how much it spends with all the major publishers, and how this translates into cost per use, and/or other indicators of value. If NPG represents poor value for money, we will work with CDL to readjust their pricing. If, as we expect, NPG represents good value for money compared with other publishers, even at the new proposed pricing, we want to work with CDL to have this reflected in our agreement. We sincerely hope that no boycotts will occur, not least because it is detrimental to the advance of science, but we will not be bullied into continuing CDL's subsidy by our other customers.

Translation: We're embarrassed and we probably will be bullied into making a much lower offer to CDL. Furthermore, we equate the advance of science with the business of publishing. It's it reduces our profits then it must be bad for science.

The one good thing that will come of this is that it will stimulate many universities to get together and form bargaining groups. That will give them a lot more clout. I'm sure all the other publishers will be thanking NGP for making this such a prominent issue.

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Why Dads Can't Dance

This is a topic that's dear to my heart? Why? Because it's one of the few things where Denyse O'Leary and I completely agree—the silliness of evolutionary psychology.

Here's her blog posting [Coffee!!! Evolution explains why Dad’s dancing is so awful, except where it isn’t]. Here's the article published in the Telegraph ['Dad dancing' may be the result of evolution, scientists claim]. The "scientist" is Peter Lovatt, a psychologist and a dancer at the University of Hertfordshire (UK).

The cringeworthy "dad dancing" witnessed at wedding receptions every weekend may be an unconscious way in which ageing males repel the attention of young women, leaving the field clear for men at their sexual peak.

"The message their dancing sends out is 'stay away, I'm not fertile'," said Dr Peter Lovatt, a psychologist at the University of Hertfordshire who has compared the dancing styles and confidence levels of nearly 14,000 people.

His research has backed up scientific studies showing a connection between dancing, hormones and sexual selection.

Men between the ages of 35 and 60 typically attempt complex moves with limited co-ordination – an observation that will be obvious to anyone who saw George W Bush shake his stuff with a troupe of West African performers in 2007.

Dr Lovatt pointed to research showing that women could gauge the testosterone levels of their dance partners by the style and energy of their moves, and suggested that "dad dancing" may be a way of warning women of child-bearing age that they might be better off looking elsewhere.

"It would seem completely unsurprising to me that since middle-aged men have passed their natural reproductive age, and probably have a family already, evolution would act to ensure they are no longer attractive to 18-year-old girls," Dr Lovatt said.

No comment is necessary except to say that psychology better do something to clean up its image or the entire discipline is going to become a joke.

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[Photo Credit: That's my daughter Jane at her wedding in June 2007. And that's me, demonstraing my infertility in the same way my cavemen ancestors might have done.]

Deepak Chopra Lecture in Toronto Has Been Cancelled

 
Deepak Chopra's lecture at the University of Toronto—the one sponsored by the Royal Ontario Museum—has been canceled [Shame on the Royal Ontario Museum]. I'd like to say that the cancellation was due to the outrage expressed by skeptics all over the world but, alas, that wasn't the reason. The lecture was canceled because of the G20 summit being held in Toronto at the end of June. The University is shutting done from June 21st to June 27th and that's why his lecture was canceled.

The good news is that there doesn't seem to be any attempt to re-schedule it. Let's hope that the Royal Ontario Museum (ROM) has come to its senses and realized that it has a public relations disaster on its hands.

CASS has sent the letter with your signatures. You can find the links on the CFI website at: CFI Expresses Dismay at ROM’s Presentation of Deepak Chopra.

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Nature vs. The University of California

 
The various campuses of the University of California subscribe to science journals by purchasing a license that allows electronic access for members of the university community, including students. The average cost of this subscription for life science journals is $4,142 per journal. Total cost for the University of California system is 24.3 million dollars per year.

Nature Publishing Group publishes 67 journals including Nature and all of the various spinoffs. The average cost for a NPG journal was $4,465 but NPG is proposing to charge $17,479 per journal next year. This is a 400% increase.

All this is explained in a letter to University of California faculty members [Informational Update on a Possible UC Systemwide Boycott of the Nature Publishing Group]. The University of California schools are dropping the subscription to all NPG journals because it can't afford such a large increase.

An article in the Chronicle of Higher Education summarizes the UC proposal [U. of California Tries Just Saying No to Rising Journal Costs]. The idea is not only to drop the subscriptions but to boycott all the NPG journals, including Nature.

Keith Yamamoto is organizing the boycott.

Keith Yamamoto is a professor of molecular biology and executive vice dean of the School of Medicine at UC-San Francisco. He stands ready to help organize a boycott, if necessary, a tactic he and other researchers used successfully in 2003 when another big commercial publisher, Elsevier, bought Cell Press and tried to raise its journal prices.

After the letter went out on Tuesday, Mr. Yamamoto received an "overwhelmingly positive" response from other university researchers. He said he's confident that there will be broad support for a boycott among the faculty if the Nature Group doesn't negotiate, even if it means some hardships for individual researchers.

"There's a strong feeling that this is an irresponsible action on the part of NPG," he told The Chronicle. That feeling is fueled by what he called "a broad awareness in the scientific community that the world is changing rather rapidly with respect to scholarly publication."

Although researchers still have "a very strong tie to traditional journals" like Nature, he said, scientific publishing has evolved in the seven years since the Elsevier boycott. "In many ways it doesn't matter where the work's published, because scientists will be able to find it," Mr. Yamamoto said.

Way to go, Keith!

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[HatTip: Janet Stemwedel]

Methodological Naturalism - How Not to Attack Intelligent Design Creationism

My philosopher friends from Ghent have published their paper ...

Boudry, M., Blancke, S., and Braeckman, J. (2010) How Not to Attack Intelligent Design Creationism: Philosophical Misconceptions About Methodological Naturalism. Foundations of Science doi:10.1007/s10699-010-9178-7.

Abstract
In recent controversies about Intelligent Design Creationism (IDC), the principle of methodological naturalism (MN) has played an important role. In this paper, an often neglected distinction is made between two different conceptions of MN, each with its respective rationale and with a different view on the proper role of MN in science. According to one popular conception, MN is a self-imposed or intrinsic limitation of science, which means that science is simply not equipped to deal with claims of the supernatural (Intrinsic MN or IMN). Alternatively, we will defend MN as a provisory and empirically grounded attitude of scientists, which is justified in virtue of the consistent success of naturalistic explanations and the lack of success of supernatural explanations in the history of science (Provisory MN or PMN). Science does have a bearing on supernatural hypotheses, and its verdict is uniformly negative. We will discuss five arguments that have been proposed in support of IMN: the argument from the definition of science, the argument from lawful regularity, the science stopper argument, the argument from procedural necessity, and the testability argument. We conclude that IMN, because of its philosophical flaws, proves to be an ill-advised strategy to counter the claims of IDC. Evolutionary scientists are on firmer ground if they discard supernatural explanations on purely evidential grounds, instead of ruling them out by philosophical fiat.

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If I Had a Billion Dollars: the Video

 
Go to Jennifer's blog and see the video. It's fantastic.

If I Had a Billion Dollars - The Video!

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If I Had a Billion Dollars

 
Stephen Harper and his cronies have spent over one billion dollars preparing for the G8 and G20 meetings in Canada this month. That's a lot of money. The city of Toronto will be pretty much shut down from June 24 to June 27. The University of Toronto will be closed on the 24th and 26th and all activities are canceled on the 21st, 22nd, and 23rd.

Here's The Bare Naked Ladies singing "If I had a million dollars" (With many interruptions). Go to Jennifer Smith's blog Runesmith's Canadian Content to see the new lyrics for [If I Had a Billion Dollars].

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Jonathan Wells Weighs in on Alternative Splicing

You can read his contribution at Evolution News & Views (sic): The Fact-Free “Science” of Matheson, Hunt and Moran: Ridicule Instead of Reason, Authority Instead of Evidence.

What I find so interesting is the willingness of Wells and Sternberg to believe whatever they find in the scientific literature. (Yeah, right.) In this case, they've found a few papers claiming that the vast majority of human genes exhibit alternative splicing. They claim this refutes the idea that introns are mostly junk.¹

Do they really believe everything that's published in the scientific literature? I don't think so. They are very selective in what they believe. They only believe the papers that criticize evolution or support their belief in intelligent design. That's why they have no credibility. That's why they deserve ridicule. That's why reasoning with an Intelligent Design Creationist is a waste of time.

Don't believe me? Try reading Icons of Evolution by Jonathan Wells. It's the example we use in my course to illustrate how NOT to do science.

Here's Wells standing up for his friend ...

So why are Matheson and Moran so sure that huge portions of introns don’t have functions? According to Matheson, it’s because “Larry Moran and I clearly know a whole lot more about molecular genetics” than Sternberg.

A more naked appeal to authority would be hard to find. It sounds like an undergraduate trying to score points in a late-night bull session (“I know all about that; I took a course in it…”), not a college professor engaged in a scientific debate.

But Matheson didn’t stop there. He demeaned Sternberg by calling him “poor Richard.” He also claimed that Sternberg is “disastrously clueless” because he doesn’t understand “the important and very basic distinction between a transcript and an intron.” Since every undergraduate biology student learns that an intron is a segment of DNA, while a transcript is a segment of RNA encoded by DNA, this last jibe is on a par with Moran’s insult that Sternberg can’t do elementary arithmetic. And it is equally unjustified.

Here's what undergraduates learn when they read what I wrote in my textbook. Maybe I should send copies to Wells and Sternberg?

Internal sequences that are removed from the primary RNA transcript are called introns. Sequences that are present in the primary transcript and in the mature RNA molecule are called exons. The words intron and exon also refer to the regions of the gene (DNA) that encode corresponding RNA introns and exons. Since DNA introns are transcribed, they are considered part of the gene.

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1. I'm ignoring the fact that Sternberg's calculation assumed that every intron in a gene must be alternatively spliced. That assumption is/was not based on anything in the scientific literature but it's unlikely that Sternberg will admit his error.

Watch This Movie

 
PZ Myers want to see Agora [I want to see this movie]. So do I. Here's the website [Agora] and here's the synopsis.

A historical drama set in Roman Egypt, concerning a slave who turns to the rising tide of Christianity in the hopes of pursuing freedom while also falling in love with his master, the famous female philosophy professor and atheist Hypatia of Alexandria.

I hear that the producers are having trouble getting widespread distribution in America. I wonder why? It's a movie about an atheist woman standing up to a Christian mob hell bent on destroying Alexandria and the library.

What's wrong with that? Sounds like Texas, or parts of Alberta.

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The Academic Discipline of Science & Religion Studies

 
Joshua Rosenau thinks that science and religion are different ways of knowing. This means that, at some level, they can't conflict. I'm a skeptic and a scientist. I want some evidence before accepting that religion offers a valid way of knowing the truth. Please give me an example of some kind of "knowing" that religion offers. Be prepared to explain why millions of atheists can get along just fine without this way of knowing. It certainly seems as though the religious way of "knowing" is completely dispensable.

While you're at it, please explain why different religions arrive at different conclusions. If religion is a valid way of knowing, then why don't all religions arrive at the same conclusions about, say, the divinity of Jesus, or the morality of abortion, or how the universe originated? If only some religions have a lock on valid ways of knowing about truth, then which ones are correct?

Josh's latest foray into this minefield is over the composition of the Science & Faith panel at the World Science Festival [A fair point]. He says, ...

In the field of science/religion studies, there's a consensus statement that's been widely circulated and agreed to, and it states: "in most instances, biology and religion operate at different and non-competing levels… natural theology may be a legitimate enterprise in its own right, but we resist the insistence of intelligent-design advocates that their enterprise be taken as genuine science - just as we oppose efforts of others to elevate science into a comprehensive world view (so-called scientism)." The New Atheists reject this consensus, as they are entitled to do. But they reject it without going through the academic literature of the relevant field, preferring pop-culture books to academic engagement.

There's so much wrong with that statement that it's hard to know where to begin. Let me just mention two problems before moving on to a third one.

1. Atheists don't believe in supernatural beings. They have not been convinced by any of the arguments offered up by religious scholars or passionate friends and relatives. This does not mean they "elevate science into a comprehensive world view (so-called scientism)." Speaking as one of those atheists, if anyone wants to argue for another valid way of knowing (other than science) then I'm more than happy to pay attention. Just don't ask me to make the assumption that supernatural beings exist. You have to convince me of that first.


2. There are perfectly valid, rational, objections to accommodationism. Josh insults all of us by saying that we don't read the academic literature. That's just not true and I expect an apology.

Finally, let's look at the so-called "consensus" view that Josh quotes. He provides a link to its source—it's the International Society for Science & Religion's Statement on the Concept of 'Intelligent Design'.

Who is this group and why should their statement be considered the consensus view in studying the possible conflicts between science and religion? Looking at their website, I find this statement about their purpose.

Our central aim is the facilitation of dialogue between the two academic disciplines of science and religion, one of the most important current areas of debate in terms of understanding the nature of humanity. This includes both the enhancement of the profile of the science-religion interface in the public eye, as well as the safeguarding of the quality and rigour of the debate in the more formal, academic arena.

Interesting. I wonder how many members are atheists and how many think that science and religion are in conflict? After all, one of the hallmarks of a true academic discipline is that it welcomes all points of view.

What do they have to say about membership?

While maintaining rigorous qualifications for membership (membership is through nomination by existing members only) the Society has now grown to over 140 members, including many of the leading scholars in the science and religion field. Indeed the last two presidents, George Ellis, a theoretical cosmologist and Professor of Applied Mathematics at the University of Cape Town, and John Polkinghorne, are both recipients of the Templeton Prize for Progress Toward Research or Discoveries about Spiritual Realities - the world's best-known religion prize, awarded each year to a living person to encourage and honour those who advance spiritual matters.

Membership of the society is truly universal: the society incorporates, and welcomes, representatives from a variety of faith traditions including Buddhism, Hinduism, Judaism, and Islam in addition to Christianity. Membership is also widely distributed geographically, with representatives from countries as diverse as South Korea, India, Australia, New Zealand and South Africa as well as from Europe and America.

Now I get it. It's a group of accommodationists. No wonder Josh thinks this is the consensus view in the field. No wonder he accuses atheists of being ignorant because they disagree with the "consensus" view of the International Society for Science & Religion.

Is this what passes for an true academic discipline in the eyes of accommodationists? No wonder we have trouble communicating.

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What Is Scientific Literacy?

 
Neil deGrasse Tyson explains it as well as anyone could. Hint: it's not about knowing the names of the planets, the valence of oxygen, or the enzymes of glycolysis.

Chad Orzel is as excited about this video as I am—and for the same reason [Neil deGrasse Tyson Agrees With Me About The Innumeracy of Intellectuals]. It's bad enough that so many people are scientifically illiterate but even worse is the fact that many of our so-called "intellectuals" are actually proud of the fact that they are stupid about mathematics and science. Last year I went to a conference on The Two Cultures where many people were trying to convince me that the problem was solved. They were wrong and I'm glad to see that Tyson agrees.

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Creationist Fairy Tales

 
Cornelius Hunter has a Ph.D. in Biophysics and Computational Biology.¹ He's an adjunct Professor at Biola University where, presumably, he teaches undergraduates.

Dr. Hunter has recently learned about transposons and this promoted him to write something on his blog, Darwin's God [Retrotransposons are not Free].

Transposons, as most of you know, are bits of selfish DNA than insert themselves into genomes. There are several different kinds of transposons but Hunter concentrates on retrotranspsons in his example. Most of the time when transposons insert themselves into a genome they cause problems because they disrupt a gene. The exceptions are those species with large genomes containing lots of junk DNA where the insertions are usually harmless.

Every now and then, a transposon will insert near, or within, a gene causing a mutation that may become beneficial. This is what caught Hunter's attention.

Consider the retrotransposons that, in addition to its promoter sequence that helps initiate the copying of its DNA into an single-stranded RNA molecule, carries its own handy reverse transcriptase gene which encodes the protein machine that copies the RNA back into a DNA molecule, for later insertion into the genome. This can certainly cause biological variation, but it is anything but free.

With evolution we must believe that so many of the sophisticated biological variation mechanisms, such as in retrotransposons, were produced by evolution. Do you see the problem? In this circular tale that even Hans Christian Andersen could never have imagined, evolution produces the intricate mechanisms that produce evolution.

Evolutionists insist that there is no problem because none of this is impossible. Why can’t evolution produce mechanisms that produce evolution? Unless one can prove this is impossible, evolution wins (an argument that goes back to the sage of Kent himself). Though the evidence fails to prove evolution, it nonetheless must be a fact. In this Alice-in-Wonderland world, that which is not false is a fact (if it is evolution, that is).

Does this sound like a fairy tale. Yes, it does. The scary part of Hunter's fairy tale is that so many people will believe it, including his students. That's more like the Grimm brothers than Hans Christian Anderson.

Seriously, there's an interesting problem here. We often make fun of the stupidity of creationists like Hunter and Richard Sternberg because they are clearly out of their depth when they write about biology and evolution. But why are their fellow creationists so silent? If it were an evolutionist writing such nonsense we would be just as critical—in fact the blogs are full of such critical debate about science.

Why aren't there any intelligent creationists who speak out against the fairy tales that permeate their blogs and their publications? Is it because there aren't any intelligent creationists? Or, is it because they are extremely reluctant to criticize their own kind? Don't they realize that their cause is being damaged by propagating nonsense?

Maybe they're not worried because they know their audience.

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1. He can't be a very good creationist because, as far as I know, he has only one Ph.D.

IDiots Do Arithmetic a Second Time - Same Result

Yesterday I wrote an article about Richard Sternberg and his lack of knowledge of molecular biology. I also took a swipe at his poor arithmetic skills, based on his misunderstanding of biology [Creationists, Introns, and Fairly Tales]. Read the comments to see why we still refer to Intelligent Design Creationists as IDiots.

Imagine my surprise when Sternberg responded with a "correction"! [Let's Do the Math Again].

Earlier today I criticized Calvin College biologist Steve Matheson’s incorrect view of “junk” DNA. Matheson had argued in February that the human genome contains about 190,000 introns (stretches of non-protein-coding DNA that interrupt protein-coding genes), of which “only a handful” had important functional roles. “How many? Oh, probably a dozen,” he wrote, “but let's be really generous. Let's say that a hundred introns in the human genome are known to have ‘important functional roles.’ Oh fine, let's make it a thousand.”

On the contrary, I pointed out that at least 90% of genes are alternatively spliced, meaning that 0.9 x 190,000 = 171,000 introns are involved in alternative splicing, an essential process that helps to ensure that the proper proteins are made at the correct developmental stage and in the appropriate cells and tissues.

Along comes University of Toronto biochemist Larry Moran, an outspoken Darwinist who hates the Center for Science and Culture so much he would probably heap abuse on us for saying that the Earth goes around the Sun. Sure enough, Moran wasted no time jumping on me for being an “Intelligent Design Creationist.” He posted the relevant portion of my critique and concluded: “It's up to you, dear readers, to figure out all the things wrong with this explanation. You can start with the math. Arithmetic isn't one of their strong points.”

A few minor corrections ...

1. I am not a Darwinist [Why I'm Not a Darwinist]
2. I don't hate the Center for Science and Culture. I mock it. It's a joke.
3. Richard Sternberg supports intelligent design and be believes in a creator who used intelligent design to create life. Therefore, he is an Intelligent Design Creationist.

So let’s do the math. Again. I will make the task easy for everyone—even Moran and Matheson:

Step 1. There are ~25,000 protein-coding genes in the human genome.
Step 2. There are 190,000 introns/25,000 protein-coding genes = 7.6 introns/gene on average.
Step 3. Ninety percent (possibly more) of gene transcripts undergo alternative splicing. Hence, 0.9 x 25,000 = 22,500 genes (actually, their RNAs) undergo alternative splicing.

Therefore, 22,500 genes x 7.6 introns/gene = 171,000 introns involved in alternative splicing.

This is just a rough estimate, of course. And as I wrote in my original critique of Matheson, even if I’m off by a factor of two we are still left with far more functional introns than Matheson acknowledges. This compels me to ask Steve Matheson: How exactly did you come up with your estimates? And what about you, Larry Moran? What sort of arithmetic are you using?

I'm using arithmetic that's based on an understanding of basic molecular biology and the scientific literature.

We could quibble about the number of introns—I think it's closer to 150,000. We could quibble about the number of protein encoding genes—the most accurate number is 20,500. We could quibble about how many genes exhibit alternative splicing—I think it's about 5%, not 95%. You can't be expected to know the facts and the controversies since this is way outside your area of expertise.

So, let's assume your facts are correct. If 90% of genes exhibit alternative splicing then this means 22,500 genes. You got that calculation right. The minimum number of introns that must be involved in alternative splicing is one (1) per gene. That means at least 22,500 introns involved in alternative splicing. You made the mistaken (and stupid) assumption that every intron in a gene had to be alternatively spliced.

The fact that you repeated this false assumption, even after being warned, does not enhance your credibility. I conclude that you don't understand RNA processing or alternative splicing. In spite of your ignorance you wrote up a posting attacking Steve Matheson and defending your colleague Steve Meyer. That's why we call you IDiots.

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Creationists, Introns, and Fairly Tales

Richard Sternberg thinks that introns are important. He has to think that way because he's an Intelligent Design Creationist and the idea that introns could be mostly junk and not have a function isn't part of his faith [Matheson’s Intron Fairy Tale].

The segments of our DNA that are commonly called "genes" consist of protein-coding exons and non-protein-coding introns. Initially, the entire DNA segment is transcribed into RNA, but between ninety and ninety-five percent of the initial RNAs are "alternatively spliced."

What is alternative splicing? Imagine that the initial RNA derived from its DNA template has the organization A—B—C—D—E—F, where the letters represent blocks that specify amino acid sequences and the dashes in between the letters stand for introns. Alternative splicing enables multiple proteins to be constructed given the same RNA precursor, say, ABCDF, ACDEF, BCDEF, and so forth. In this way, hundreds or thousands of proteins can be derived from a single gene.

There’s more. The messenger RNAs that are produced by this process—and therefore the proteins that are made in a cell—are generated in a way that depends on the stage of development as well as the cell and tissue type. In the above example, a nerve cell may express the ACDEF version of a messenger RNA whereas a pancreatic cell may produce only the BCDE version. The differences are biologically essential.

What does this have to with introns? Everything. It is the presence of introns that makes this permutative expansion of messenger RNAs possible in the first place.

So let’s do the math. At least ninety percent of gene transcripts undergo alternative splicing, and there are at least 190,000 introns in the human genome. That means we have at least 0.90 x 190,000 = 171,000 introns that participate in the alternative-splicing pathway(s) available to a cell.

It's up to you, dear readers, to figure out all the things wrong with this explanation. You can start with the math. Arithmetic isn't one of their strong points. Or maybe it's an understanding of biology that's the real weak point?

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